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Namespaces | Functions
frags Namespace Reference

Namespaces

 ABEGO
 
 contacts
 
 nonlocal
 
 picking
 
 scoring
 

Functions

BooleanOptionKey const frags ("frags")
 
IntegerOptionKey const j ("frags:j")
 
BooleanOptionKey const filter_JC ("frags:filter_JC")
 
BooleanOptionKey const bounded_protocol ("frags:bounded_protocol")
 
BooleanOptionKey const keep_all_protocol ("frags:keep_all_protocol")
 
BooleanOptionKey const quota_protocol ("frags:quota_protocol")
 
BooleanOptionKey const nonlocal_pairs ("frags:nonlocal_pairs")
 
BooleanOptionKey const fragment_contacts ("frags:fragment_contacts")
 
BooleanOptionKey const p_value_selection ("frags:p_value_selection")
 
IntegerOptionKey const n_frags ("frags:n_frags")
 
FileOptionKey const allowed_pdb ("frags:allowed_pdb")
 
StringVectorOptionKey const ss_pred ("frags:ss_pred")
 
FileOptionKey const spine_x ("frags:spine_x")
 
FileOptionKey const depth ("frags:depth")
 
FileOptionKey const denied_pdb ("frags:denied_pdb")
 
IntegerVectorOptionKey const frag_sizes ("frags:frag_sizes")
 
BooleanOptionKey const write_ca_coordinates ("frags:write_ca_coordinates")
 
BooleanOptionKey const write_scores ("frags:write_scores")
 
BooleanOptionKey const annotate ("frags:annotate")
 
IntegerOptionKey const nr_large_copies ("frags:nr_large_copies")
 
IntegerOptionKey const n_candidates ("frags:n_candidates")
 
BooleanOptionKey const write_rama_tables ("frags:write_rama_tables")
 
RealOptionKey const rama_C ("frags:rama_C")
 
RealOptionKey const rama_B ("frags:rama_B")
 
RealOptionKey const sigmoid_cs_A ("frags:sigmoid_cs_A")
 
RealOptionKey const sigmoid_cs_B ("frags:sigmoid_cs_B")
 
RealOptionKey const seqsim_H ("frags:seqsim_H")
 
RealOptionKey const seqsim_E ("frags:seqsim_E")
 
RealOptionKey const seqsim_L ("frags:seqsim_L")
 
RealOptionKey const rama_norm ("frags:rama_norm")
 
StringOptionKey const describe_fragments ("frags:describe_fragments")
 
RealOptionKey const picking_old_max_score ("frags:picking_old_max_score")
 
BooleanOptionKey const write_sequence_only ("frags:write_sequence_only")
 
BooleanOptionKey const output_silent ("frags:output_silent")
 
BooleanOptionKey const output_index ("frags:output_index")
 
BooleanOptionKey const score_output_silent ("frags:score_output_silent")
 

Function Documentation

FileOptionKey const frags::allowed_pdb ( "frags:allowed_pdb"  )

Referenced by register_options().

BooleanOptionKey const frags::annotate ( "frags:annotate"  )
BooleanOptionKey const frags::bounded_protocol ( "frags:bounded_protocol"  )

Referenced by register_options().

FileOptionKey const frags::denied_pdb ( "frags:denied_pdb"  )

Referenced by register_options().

FileOptionKey const frags::depth ( "frags:depth"  )
StringOptionKey const frags::describe_fragments ( "frags:describe_fragments"  )

Referenced by register_options().

BooleanOptionKey const frags::filter_JC ( "frags:filter_JC"  )
IntegerVectorOptionKey const frags::frag_sizes ( "frags:frag_sizes"  )

Referenced by register_options().

BooleanOptionKey const frags::fragment_contacts ( "frags:fragment_contacts"  )
BooleanOptionKey const frags::frags ( "frags"  )
IntegerOptionKey const frags::j ( "frags:j"  )

Referenced by register_options().

BooleanOptionKey const frags::keep_all_protocol ( "frags:keep_all_protocol"  )

Referenced by main(), and register_options().

IntegerOptionKey const frags::n_candidates ( "frags:n_candidates"  )

Referenced by register_options().

IntegerOptionKey const frags::n_frags ( "frags:n_frags"  )

Referenced by register_options().

BooleanOptionKey const frags::nonlocal_pairs ( "frags:nonlocal_pairs"  )

Referenced by register_options().

IntegerOptionKey const frags::nr_large_copies ( "frags:nr_large_copies"  )
BooleanOptionKey const frags::output_index ( "frags:output_index"  )
BooleanOptionKey const frags::output_silent ( "frags:output_silent"  )
BooleanOptionKey const frags::p_value_selection ( "frags:p_value_selection"  )

Referenced by main().

RealOptionKey const frags::picking_old_max_score ( "frags:picking_old_max_score"  )
BooleanOptionKey const frags::quota_protocol ( "frags:quota_protocol"  )

Referenced by main(), and register_options().

RealOptionKey const frags::rama_B ( "frags:rama_B"  )
RealOptionKey const frags::rama_C ( "frags:rama_C"  )
RealOptionKey const frags::rama_norm ( "frags:rama_norm"  )
BooleanOptionKey const frags::score_output_silent ( "frags:score_output_silent"  )
RealOptionKey const frags::seqsim_E ( "frags:seqsim_E"  )
RealOptionKey const frags::seqsim_H ( "frags:seqsim_H"  )
RealOptionKey const frags::seqsim_L ( "frags:seqsim_L"  )
RealOptionKey const frags::sigmoid_cs_A ( "frags:sigmoid_cs_A"  )
RealOptionKey const frags::sigmoid_cs_B ( "frags:sigmoid_cs_B"  )
FileOptionKey const frags::spine_x ( "frags:spine_x"  )
StringVectorOptionKey const frags::ss_pred ( "frags:ss_pred"  )

Referenced by register_options().

BooleanOptionKey const frags::write_ca_coordinates ( "frags:write_ca_coordinates"  )

Referenced by register_options().

BooleanOptionKey const frags::write_rama_tables ( "frags:write_rama_tables"  )
BooleanOptionKey const frags::write_scores ( "frags:write_scores"  )
BooleanOptionKey const frags::write_sequence_only ( "frags:write_sequence_only"  )